Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references. / The geographic distribution and dynamics of coastal benthic populations are shaped by physical - biological interactions affecting larval dispersal and the demography of juvenile and adult individuals. This thesis focused on nearshore patterns of larval distribution and regional patterns in demography of intertidal barnacles in Southern and Baja California. Horizontal and vertical distributions, and the mortality rates of larvae, were assessed from short term (i.e. days) small- scale observations (0.1-1 km) in nearshore waters. Observations on spatial variability of adult barnacle demography were gathered over 1.5 years at scales of hundreds of kilometers. Stage-specific horizontal distributions and nearshore current measurements suggested that larvae of Balanus g-landula and Chthamalus spp. may experience limited dispersal. High mortality rates could further limit travel distances and the exchange of individuals among disjunct populations. Data on vertical distributions indicated that nauplii and cyprids of Balanus nubilus and Pollicipes polymerus occur at different depths. Nauplii remained near the surface at all times, whereas cyprids occurred in the bottom half of the water column. / (cont.) Such distributions, combined with vertical variability in horizontal flows, might cause the observed horizontal segregation of nauplii and cyprids. Differences in survival, growth rate, size structure, and per capita fertility of adult Balanus glandula were observed between Dana Point (Southern California) and Punta Baja (Baja California), a site located near the species' southern limit of distribution. Effects of spatial differences in demography on population persistence were assessed with a stage-structured matrix model. Model analyses indicated that the Punta Baja population is more susceptible to environmental stochasticity and more prone to local extinction than populations located further north. This thesis emphasizes the importance of characterizing factors that affect the dynamics of benthic populations at multiple spatial-temporal scales, and the usefulness of small scale high- frequency observations of nearshore phenomena, especially in relation with the dispersal of larvae. / by Fabián J. Tapia. / Ph.D.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and the Woods Hole Oceanographic Institution), 2006. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Also issued in pages. Barker Engineering Library copy: issued in pages. / Includes bibliographical references (leaves 193-[201]). / The first part of the dissertation investigates the application of the theory of large random matrices to high-dimensional inference problems when the samples are drawn from a multivariate normal distribution. A longstanding problem in sensor array processing is addressed by designing an estimator for the number of signals in white noise that dramatically outperforms that proposed by Wax and Kailath. This methodology is extended to develop new parametric techniques for testing and estimation. Unlike techniques found in the literature, these exhibit robustness to high-dimensionality, sample size constraints and eigenvector misspecification. By interpreting the eigenvalues of the sample covariance matrix as an interacting particle system, the existence of a phase transition phenomenon in the largest ("signal") eigenvalue is derived using heuristic arguments. This exposes a fundamental limit on the identifiability of low-level signals due to sample size constraints when using the sample eigenvalues alone. The analysis is extended to address a problem in sensor array processing, posed by Baggeroer and Cox, on the distribution of the outputs of the Capon-MVDR beamformer when the sample covariance matrix is diagonally loaded. / (cont.) The second part of the dissertation investigates the limiting distribution of the eigenvalues and eigenvectors of a broader class of random matrices. A powerful method is proposed that expands the reach of the theory beyond the special cases of matrices with Gaussian entries; this simultaneously establishes a framework for computational (non-commutative) "free probability" theory. The class of "algebraic" random matrices is defined and the generators of this class are specified. Algebraicity of a random matrix sequence is shown to act as a certificate of the computability of the limiting eigenvalue distribution and, for a subclass, the limiting conditional "eigenvector distribution." The limiting moments of algebraic random matrix sequences, when they exist, are shown to satisfy a finite depth linear recursion so that they may often be efficiently enumerated in closed form. The method is applied to predict the deterioration in the quality of the sample eigenvectors of large algebraic empirical covariance matrices due to sample size constraints. / by Rajesh Rao Nadakuditi. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2009. / Includes bibliographical references. / Trichodesmium spp. are considered the dominant nitrogen (N) fixing cyanobacteria in tropical and subtropical oceans, regimes frequently characterized by low iron (Fe). Limited information exists about what levels of Fe limit Trichodesmium N fixation. I developed a diagnostic for Fe limitation using quantitative reverse transcription PCR (qRT-PCR) of the Fe stress response gene isiB, which encodes for flavodoxin a non-Fe containing substitute for ferredoxin. I determined that high isiB gene expression corresponded to cell-specific reductions in N fixation rates in both phylogenetic clades of Trichodesmium grown on varying levels of Fe. Using these laboratory-determined thresholds, I assessed Fe limitation of Trichodesmium from the Sargasso Sea, equatorial Atlantic Ocean and Western Pacific Warm Pool in conjunction with other analytical measurements (N, phosphorus (P) and dissolved Fe (<0.4[mu]m filtered)). I found widespread Fe limitation in Trichodesmium from the Pacific Ocean and minimal expression in the North Atlantic Ocean. I also found an inverse correlation between isiB expression and dissolved Fe:P ratios in seawater and data suggesting that most dissolved Fe in seawater, including organic ligand-bound Fe, is available to Trichodesmium. These data support and refine previous model predictions and demonstrate, in situ, the importance of Fe to the marine N cycle. / by Phoebe Dreux Chappell. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references. / Two years of moored oceanographic and automatic weather station data which span the winter ice seasons of 2001-2003 within Marguerite Bay on the western Antarctic Peninsula (wAP) shelf were collected as part of the Southern Ocean Global Ocean Ecosystems Dynamics program. In order to characterize the ice environment in the region, a novel methodology is developed for determining ice coverage, draft and velocity from moored upward-looking acoustic Doppler current profiler data. A linear momentum balance shows the importance of internal ice stresses in the observed motion of the ice pack. Strong inertial, not tidal, motions were observed in both the sea ice and upper ocean. Estimates of upward diapycnal fluxes of heat and salt from the Upper Circumpolar Deep Water to the surface mixed layer indicate almost no contribution from double diffusive convection. A one-dimensional vertical mixed layer model adapted for investigation of mixing beneath an ice-covered ocean indicates that the initial wind event, rather than subsequent inertial shear, causes the majority of the mixing. This work points towards episodic wind-forced shear at the base of the mixed layer coupled with static instability from brine rejection due to ice production as a major factor in mixing on the wAP shelf. / by Jason Hyatt. / Ph.D.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (leaves 70-72). / The uncertainty in the determination of the momentum and scalar fluxes remains one of the main obstacles to accurate numerical forecasts in low to moderate wind conditions. For example, latent heat fluxes computed from data using direct covariance and bulk aerodynamic methods show that there is good agreement in unstable conditions when the latent heat flux values are generally positive. However, the agreement is relatively poor in stable conditions, particularly when the moisture flux is directed downward. If the direct covariance measurements are indeed accurate, then they clearly indicate that the bulk aerodynamic formula overestimate the downward moisture flux in stable conditions. As a result, comparisons of the Dalton number for unstable and stable conditions indicate a marked difference in value between the two stability regimes. Investigations done for this thesis used data taken primarily at the Air-Sea Interaction Tower (ASIT) during the Coupled Boundary Layers and Air-Sea Transfer (CBLAST) Experiment 2003 from the 20-27 August 2003. Other data from the shore based Martha's Vineyard Coastal Observatory (MVCO) and moored buoys in the vicinity of the ASIT were also incorporated. / (cont.) During this eight day period, the boundary layer was often characterized by light winds, a stably stratified surface layer and a swell dominated wave field. Additionally, the advection of warm moist air over cooler water resulted in fog formation and a downward flux of moisture on at least three occasions. Therefore, a primary objective of this thesis is to present a case study to investigate the cause of this shortcoming in the bulk formula under these conditions by examining the physical processes that are unique to these boundary layers. Particular attention will be paid to the behavior of the Dalton number in a stable marine atmospheric boundary layer under foggy conditions using insights derived from the study of fog formation and current flux parameterization methods. / by Robert Farrington Crofoot. / S.M.

Thesis (S.M.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 63-65). / Hydrothermal vents discharge superheated, mineral rich water into our oceans, thereby providing a habitat for exotic chemosynthetic biological communities. Hydrothermal fluids are convected upwards until they cool and reach density equilibrium, at which point they advect laterally with the current. The neutrally buoyant plume layer can have length scales on the order of several kilometers, and it therefore provides the best means to detect the presence of vent fields on the seafloor, which typically have length scales on the order of a few meters. This thesis uses field measurements of the velocity, temperature and particulate anomalies associated with the TAG hydrothermal plume to demonstrate that tidal currents exert a strong impact on the plume shape, and to provide new constraints on the thermal power of the TAG hydrothermal system. The results show that the power output of the TAG system is on the order of 6000 MW, which is up to two orders of magnitude greater than previous estimates, and that there is considerably more entrainment than had previously been assumed. / by Sacha Wichers. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2006. / Includes bibliographical references (p. 297-311). / The physical and biological forces that drive zooplankton distribution and patchiness in an antarctic continental shelf region were examined, with particular emphasis on the Antarctic krill, Euphausia superba. This was accomplished by the application of acoustic, video, and environmental sensors during surveys of the region in and around Marguerite Bay, west of the Antarctic Peninsula, in the falls and winters of 2001 and 2002. An important component of the research involved the development and verification of methods for extracting estimates of ecologically-meaningful quantities from measurements of scattered sound. The distribution of acoustic volume backscattering at the single frequency of 120 kHz was first examined as an index of the overall biomass of zooplankton. Distinct spatial and seasonal patterns were observed that coincided with advective features. Improved parameterization was then achieved for a theoretical model of Antarctic krill target strength, the quantity necessary in scaling measurements of scattered sound to estimates of abundance, through direct measurement of all necessary model parameters for krill sampled in the study region and survey period. / (cont.) Methods were developed for identifying and delineating krill aggregations, allowing the distribution of krill to be distinguished from that of the overall zooplankton community. Additional methods were developed and verified for estimating the length, abundance, and biomass of krill in each acoustically-identified aggregation. These methods were applied to multi-frequency acoustic survey data, demonstrating strong seasonal, inter-annual, and spatial variability in the distribution of krill biomass. Highest biomass was consistently associated with regions close to land where temperatures at depth were cool. Finally, the morphology, internal structure, and vertical position of individual krill aggregations were examined. The observed patterns of variability in aggregation characteristics between day and night, regions of high versus low food availability, and in the presence or absence of predators, together reinforced the conclusion that aggregation and diel vertical migration represent strategies to avoid visual predators, while also allowing the krill access to shallowly-distributed food resources. The various findings of this work have important implications to the fields of zooplankton acoustics and Antarctic krill ecology, especially in relation to the interactions of the krill with its predators. / by Gareth L. Lawson. / Ph.D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2007. / Includes bibliographical references (p. 43-45). / Grain size is an important material property that has significant effects on the viscosity, dominant deformation mechanism, attenuation, and shear wave velocity of the oceanic upper mantle. Several studies have investigated the kinetics of grain size evolution, but have yet to incorporate these evolution equations into large-scale flow models of the oceanic upper mantle. We construct self-consistent 1.5-D steady-state Couette flow models for the oceanic upper mantle to constrain how grain size evolves with depth assuming a composite diffusion-dislocation creep rheology. We investigate the importance of water content by examining end-member models for a dry, wet, and dehydrated mantle (with dehydration above -60-70 km depth). We find that grain size increases with depth, and varies with both plate age and water content. Specifically, the dehydration model predicts a grain size of -11 mm at a depth of 150 km for 75 Myr-old oceanic mantle. This results in a viscosity of -1019 Pa s, consistent with estimates from geoid and glacial rebound studies. We also find that deformation is dominated by dislocation creep beneath -60-70 km depth, in agreement with observations of seismic anisotropy in the oceanic upper mantle. The calculated grain size profiles are input into a Burger's model system to calculate seismic quality factor (Q) and shear wave velocity (Vs). For ages older than 50 Myrs, we find that Q and Vs predicted by the dehydration case best match seismic reference models for Q and the low seismic shear wave velocity zone (LVZ) observed in the oceanic upper mantle. / by James R. Elsenbeck, II. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 239-244). / In biology, the importance of fluid drag, diffusion, and heat transfer both internally and externally, suggest the boundary layer as an important subject of investigation, however, the complexities of biological systems present significant and unique challenges to analysis by experimental fluid dynamics. In this investigation, a system for automatically profiling the boundary layer over free-swimming, deforming bodies was developed and the boundary layer over rigid and live mackerel, bluefish, scup and eel was profiled. The profiling system combined robotics, particle imaging velocimetry, a custom particle tracking code, and an automatic boundary layer analysis code. Over 100,000 image pairs of flow in the boundary layer were acquired in swimming fish alone, making spatial and temporal ensemble averaging possible. A flat plate boundary layer was profiled and compared to known laminar and turbulent boundary layer theory. In general, profiles resembled those of Blasius for sub-critical length Reynolds numbers, Rex. Transition to a turbulent boundary layer was observed near the expected critical Rex and subsequent profiles agreed well with the law of the wall. The flat plate analysis demonstrated that the particle tracking and boundary layer analysis algorithms were highly accurate. / (cont.) In rigid fish, separation of flow was clearly evident and the boundary layer transitioned to turbulent at lower Rex than in swimming fish and the flat plate. Wall shear stress, [tao]o, forward of separation was slightly higher than flat plate values. Friction drag in rigid and swimming fish was determined by integrating [tao]o over the surface of the fish. The analysis was facilitated by the definition of the relative local coefficient of friction. In general, there was no significant difference in friction drag between the rigid-body and swimming cases. In swimming, separation was, on average, delayed. Therefore, pressure drag was estimated on the basis of thickness ratio and used to calculate an upper-bound total drag on a swimming fish. Total drag was used to determine the required muscle power output during swimming and compare that with existing muscle power data. [tau]o and boundary layer thickness oscillated with undulatory phase. The magnitude of oscillation appears to be linked to body wave amplitude. / by Erik J. Anderson. / Ph.D.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references. / Studying the social and cultural transmission of behavior among animals helps to identify patterns of interaction and information content flowing between individuals. Killer whales are likely to acquire traits culturally based on their population-specific feeding behaviors and group-distinctive vocal repertoires. I used digital tags to explore the contributions of individual Norwegian killer whales to group carousel feeding and the relationships between vocal and non-vocal activity. Periods of tail slapping to incapacitate herring during feeding were characterized by elevated movement variability, heightened vocal activity and call types containing additional orientation cues. Tail slaps produced by tagged animals were identified using a rapid pitch change and occurred primarily within 20m of the surface. Two simultaneously tagged animals maneuvered similarly when tail slapping within 60s of one another, indicating that the position and composition of the herring ball influenced their behavior. Two types of behavioral sequence preceding the tight circling of carousel feeding were apparent. First, the animals engaged in periods of directional swimming. They were silent in 2 of 3 instances, suggesting they may have located other foraging groups by eavesdropping. Second, tagged animals made broad horizontal loops as they dove in a manner consistent with corralling. All 4 of these occasions were accompanied by vocal activity, indicating that this and tail slapping may benefit from social communication. No significant relationship between the call types and the actual movement measurements was found. Killer whale vocalizations traditionally have been classified into discrete call types. Using human speech processing techniques, I considered that calls are alternatively comprised of shared segments that can be recombined to form the stereotyped and variable repertoire. / (cont.) In a classification experiment, the characterization of calls using the whole call, a set of unshared segments, or a set of shared segments yielded equivalent performance. The shared segments required less information to parse the same vocalizations, suggesting a more parsimonious system of representation. This closer examination of the movements and vocalizations of Norwegian killer whales, combined with future work on ontogeny and transmission, will inform our understanding of whether and how culture plays a role in achieving population-specific behaviors in this species. / by Ari Daniel Shapiro. / Ph.D.